Naruto No Rin'negan
by Mike-Parrott
Summary: After VotE Naruto acquires the Rin'negan and starts the quest to become the most powerful ninja in the naruto universe. Nagato-trained Naruto? and Naruto/Konan. Will have lemons in future chapters.
1. Chapter 1: The Awakening

Naruto No Rin'negan

By Mike-Parrott

Chapter 1: The Awakening

**(A/N This is my first ever story and wouldn't mind if you told me how it is. The pairing will be Naruto/Konan because well I love this pairing.)**

"Somebody Talking"

'_Somebody Thinking'_

"**Demon Talking"**

'_**Demon Thinking'**_

The story starts with our yellow-haired Jinchuuriki*, Naruto Uzumaki at Valley of the End with his rival Sasuke Uchiha. Both Shinobi* were in their special forms, Naruto Using the power of the Kyuubi* and Sasuke using the power of his cursed seal.

"Valley of the End. This is the perfect setting, isn't it Naruto?" Said Sasuke. Naruto wouldn't reply to the Uchiha he was too angry at him. "Yes... that's right, like I said the time for talk is over. Well finally it's ending. This battle. The battle...Until now...From now on."

"CHIDORI!" The Uchiha had his signature jutsu ready to strike. "RASENGAN!" The Uzumaki had his signature jutsu ready to strike as well. They both leapt off the rocks and went to strike one another. That's when it happened their jutsu's struck each other causing a massive surge of chakra to envelop both of the shinobi. Sasuke's Chidori* struck Naruto's chest, while Naruto's Rasengan* scratched Sasuke's Hitae-ate*.

The Chakra died down. And the two Genins* fell onto the side of the waterfall. Naruto had struck the floor lying on his back. Sasuke was still standing, and was looking over Naruto. His Hitae-ate fell off his forehead and landed next to Naruto. "Naruto...I..." Rain started to fall and Sasuke took his leave from the fire country to go to Orochimaru.

"Naruto..." Kakashi had made his way to the Valley of the End and only saw Naruto on the floor with a hole in his jumpsuit. "I'm sorry...was your fate...Death?" Kakashi questioned.

Naruto started to open his eyes slowly and saw Kakashi looking over him with Pakkun. "Where's Sasuke, Kakashi-Sensei?" Kakashi's head lowered.

"I'm sorry Naruto, but I think he's gone. I'm sorry, let's get back to the village." When Kakashi said this he saw Naruto's eyes. They weren't the blue eyes he'd came accustomed with, they were lavender coloured with concentric circles with one black pupil. "Naruto, what's wrong with your eyes?"

"What are you talking about Kakashi-Sensei, are they the Kyuubi's eyes?" questioned Naruto. When Kakashi heard this he got a scroll out of his flak jacket and un-sealed a hand mirror and passed it to Naruto. "Have a look yourself, Naruto." When Naruto looked into the mirror he was amazed his eyes weren't his or the Kyuubi's they were a new type of eyes, he'd never seen something like his eyes before.

"Kakashi-Sensei? What's wrong with my eyes?" Naruto was confused, this was probably the weirdest thing that's happened to him, and he was the Kyuubi Jinchuuriki. "Well I've heard about it in stories and legends, it was called the Rin'negan*, and in folk legend the only person to have those eyes was the Rikudō Sennin*, he was known as the creator of Ninjutsu and was known as the messiah. Those eyes, the Rin'negan are known as the most powerful Doujutsu and are even stronger than the Sharingan*."

When Naruto heard this he was ecstatic, he had the most powerful eyes in the world, even stronger than Sasuke's Sharingan. "So I can be even stronger now because of these eyes?" Naruto had regained his strength and was jumping around about his new power. "Naruto, you could be one of the most powerful shinobi in the world because of them. But don't just rely on those eyes; I have seen many Uchihas who think they are the stronger due to their eyes. You need to promise to me that you won't just rely on those eyes, right Naruto?"

"Yes Kakashi-Sensei!" Shouted Naruto while doing a mock salute. When Kakashi heard this he summoned Pakkun. "Pakkun, I need you to find Jiraiya and tell him about the Valley of the End and Naruto's Rin'negan, got it?" Pakkun nodded and ran away quicker than Kakashi and Naruto. When Kakashi and Naruto left, a plant-like man came out of the floor and started talking to itself. "That was unexpected, I wouldn't believe there would be another Rin'negan user than Leader-Sama, I should report this immediately."

~~Akatsuki Headquarters~~

"The Kyuubi Jinchuuriki has acquired the Rin'negan." When the plant-like man named Zetsu said this, the whole cave went in to an uproar about the Uzumaki. There was constant shouting with each other for a minute until the leader put his hand up and everybody went silent. " I never knew the Uzumaki clan had the Rin'negan as well, only the Rikudō Sennin and I have got it. This is going to be trickier than I expected. Konan!" when the leader shouted this another hologram went next to the leader. "You and I will find the Uzumaki and capture him and take him to Amegakure*, ok?" The leader whispered this to Konan and they went their separate ways. "In three years we will start capturing the Bijuu, Dismissed."

~~Amegakure~~

"Konan, I am going to train this boy how to use his Rin'negan effectively, I don't think Jiraiya-Sensei will mind if we take him for a three-year training trip." Konan grinned after hearing this; she wanted to see her sensei for the first time in over 10 years. "Konan, we will do no harm to Naruto, I don't think family should attack one another don't you think." The leader called Pein was smirking.

A/N what do you think? This is my first ever story and I don't know how good it is. This is going to have lots of chapters and I'll probably write a new chapter once every couple of weeks. I've made Pein and Konan OOC because I want a Nagato-trained Naruto and Naruto/Konan. And **SPOILERS** Nagato and Naruto are related in the latest manga chapters so I thought I'd make Nagato know about his heritage. Please review!

Japanese meanings:

Jinchuuriki: Power of human sacrifice, these are holders of the bijuu such as Gaara and Naruto.

Shinobi: means ninja.

Kyuubi: Nine-tailed Fox. The beast which is kept in Naruto.

Chidori: 1.000 birds. Kakashi's first technique he created, A-rank lightning Ninjutsu.

Rasengan: Spiraling Sphere. Created by The Fourth Hokage when observing the Bijuu bomb. A-rank ninjutsu.

Hitae-ate: Headand. The ninja forehead protecters used ny every ninja to represent their village.

Genin: The lowest rank of a ninja. Consisting of Jonin, Chuunin and Genin.

Rin'negan: Samsara eye. A very rare doujutsu only been wielded by the sage of six paths and Nagato Uzumaki.

Rikudō Sennin: The sage Of Six Paths. The first user of ninjutsu and the ex-Juubi jinchuuriki.

Sharingan: Copy Wheel eye. Doujutsu used by the Uchiha clan.

Amegakure: The Village hidden in rain. Leader is Nagato.


	2. Chapter 2: The Training trip

Naruto No Rin'negan

By Mike-Parrott

Chapter 2: The three year trip

(A/N I was bored so I've started to write more chapters of this story. Nagato and Konan will be training Naruto for the three years and I won't be skipping it like many other stories do, the information will be beneficial and well this story will be quite big. And yes the start of last chapter was actually what was said in the manga :P but anyway lets commence with CHAPTER:2!)

"Somebody Talking"

'_Somebody Thinking'_

"**Demon Talking"**

'_**Demon Thinking'**_

~~Amegakure~~

"Nagato, when are we setting off to find the Uzumaki?" questioned Konan, she never knew Nagato had any living relatives and it was the Kyuubi Jinchuuriki, Naruto Uzumaki. "Jiraiya-Sensei will have found out about Naruto's Rin'negan by now and will try and train him like how he trained me in our earlier days. We should set off as soon as possible."

"So we have three years with the Uzumaki, ay? I always wanted another shinobi who knew the art of Origami!" Konan said while grinning. This was going to be a good three years.

~~Konohagakure~~

Naruto and Kakashi had just made it to the front gate of Konoha, Naruto could see two of the legendary Sannin* waiting for him, Jiraiya and Tsunade. When Tsunade saw a glimpse of spiky-yellow hair she dashed to it and hugged the owner of the yellow hair. "Baa-Chan...Your choking me..." Naruto was trying to say whilst he had the blonde Hokage all over him (A/N not what you think ;P)

"Hahaha Tsunade, you could have gave the Kiroii No Senko* a run for his money with that speed." Said the self-proclaimed biggest pervert ever, Jiraiya the Toad sage. When she heard this she got off Naruto and hit Jiraiya over the heard, but because of her inhumane strength he slammed into the floor, face-first. "Whoops."

Jiraiya got out of the ditch and started to stare at Naruto's new eyes. _'So Kakashi was Right.'_ Jiraiya stopped staring at his eyes and started to tell Naruto of his plan "Naruto, you and I are going to go on a little training trip; I will make you so strong Akatsuki won't be able to touch you!" Naruto started to smile and was getting excited about his future strength and power.

"But Naruto, we will be gone for three years, you shouldn't doubt me though, I once taught somebody with the same eyes as yours in Amegakure, His name was Nagato." When Naruto heard this he became extremely confused.

"But Kakashi-Sensei said only me and the Rikudō Sennin have had the Rin'negan, and your saying you taught somebody with the same eyes. And you couldn't have taught the Rikudō Sennin. "

"Kakashi said that because he didn't know about this boy, but now he's dead and you're the only Rin'negan user left. He would have been a big help, I heard he became extremely talented with the Rin'negan he was also presumed to be the Child of Prophecy!"

"The Child of Prophecy?" Naruto questioned, this had been an extremely confusing day for Naruto.

"Never mind Gaki, so pack your bags and let's get going, we don't control time and we need to hurry."

It only took Naruto five minutes to pack everything, the last time Jiraiya had saw him he had taught him how to use storage seals. But there wasn't that much to pack anyway. "Ero-Sennin let's get going!"

"You were quick Gaki, are you that pumped up for the training? Is it because of the extreme strength and power you will receive in the next three years?" Naruto started to nod enthusiastically.

"Hell yeah! The more time we have, the quicker I can bring Sasuke back!" When Jiraiya heard this he frowned. He didn't want Naruto end up like him when he was friends with Orochimaru.

~FLASHBACK~

Jiraiya and Orochimaru were in a forest full of extremely big trees in standard Jonin clothes, Jiraiya looked exhausted while Orochimaru was grinning evilly. "Why...Why are you...we, who are called the Sannin...We have been companions since we were children, haven't we?" Jiraiya said he was too exhausted to finish this fight with his friend

Kukuku...You'll always be a simple person, Jiraiya. Whatever your thinking, it won't work. Because you aren't aware of what I was doing..." said Orochimaru He was grinning sadistically at his injured ex-comrade.

"Think again about what you're doing...Orochimaru..." Jiraiya said still to exhausted trying to bring Orochimaru back with words.

"You're Pitiful. You're nothing but a fool!" Shouted Orochimaru while running to Jiraiya's location

~END FLASHBACK~

"Forget about Sasuke, he went to Orochimaru willingly, he won't be coming back. Don't try and say anything else, Naruto. If he was your friend why would he use an A-Rank jutsu on you?"

Naruto was speechless; he couldn't say anything back to Jiraiya.

"Lets get going Naruto, and please try and forget about bringing Sasuke, you don't want to turn out like me!" Jiraiya said smiling. This in turn made Naruto smile at the older man's antics.

~~Outside Konoha~~

"Ok, what are we going to do first Ero-Sennin, how to do Chidori? How to summon ramen?" Naruto was really ecstatic when it came to learning Jutsu.

"No because of your Rin'negan you should be able to have all six forms of nature manipulation and I'm just going to check if I'm right, If I am, I will teach you one jutsu for each element at the moment." When he said this he brought out a piece of paper.

"Naruto, this is chakra-paper. When you put chakra into this paper the paper will react to your elemental nature. If its water the paper will become damp, if its fire the paper will burst into flames, if its earth the paper will crumble, if its wind the paper will cut into two, and if it's lightning the paper will crumple."

"Ok, here goes Ero-Sennin!" Naruto poured his chakra into the paper, and to Jiraiya's assumption the paper did all 5 reactions.

"So Naruto my assumption was correct, you will be able to learn every jutsu in the wor-" Jiraiya was cut off by a piece of paper going past him, when he turned around to see who threw it at him, and he saw two people dressed in Akatsuki cloaks. One had Spiky-orange hair with several studs connected to his face; he also had the same eyes as Naruto, the Rin'negan. He looked extremely familiar to the Toad sage.

And the other person had dark-blue hair with a white, origami flower in her hair; her eyes were the same colour as her hair, Jiraiya knew who this was so again, his assumption was correct but was flabbergasted with his assumption.

"I thought you two were dead, Yahiko*, Konan. Where have you been I haven't seen you since the ninja world war? I heard you guys had died, and where's Nagato? Jiraiya was extremely confused to see those two without their other friend Nagato, but he was also confused about Yahiko having the Rin'negan _'He didn't kill Nagato and steal them I hope'_

"Hello, Jiraiya-Sensei. Long time no see, ay?" said Konan she was smirking at Jiraiya's confused face.

"Jiraiya, we have come here to take the Uzumaki. And no were not going to do what you think, Konan and I are going to train Naruto how to use the Rin'negan to become the most powerful shinobi in the world. And Jiraiya-Sensei, Nagato is not dead but Yahiko is, this is one of the powers of the Rin'negan he is one of my six bodies I use due to me being incapacitated."

Jiraiya felt better that his questions had been answered but was still unsure about letting 'Nagato' and Konan take the boy, this could be all a ploy so they could have the Kyuubi and extract it for Akatsuki.

"Even though this is the worst decision I have ever made. I'm sorry Naruto go with those tow, they won't hurt you I hope." When Jiraiya said this Naruto looked confused at his Sensei but went along with his orders and went to the other two.

"Jiraiya-Sensei, we will meet you in three years in Amegakure so you can have the Uzumaki back, I assure you we will not harm the boy, but when he returns he will be stronger than you will ever expect, We will send a messenger toad every month about Akatsuki and Naruto. Goodbye Jiraiya-Sensei." When 'Nagato said this Konan, Naruto and 'Nagato' shunshin'ed away back to Amegakure.

"Become strong...Naruto."

A/N what do you think? The Naruto and Konan pairing won't properly start until after the three years training, I don't know how old Konan is probably in late 30's? But in this she will be 24? And Naruto's age will be bumped up to 18 after the training trip.

But yeah how do you guys like this? Please review!

If you don't know Nagato was using his Yahiko path that's why Jiraiya was confused.

Japanese Translations:

Sannin: Legendary Three. Consists of Tsunade, Jiraiya and Orochimaru, given the name by Hanzo.

Kiroii No Senko: The yellow Flash. Nickname for Minato Namikaze, The fourth Hokage while in the Third Ninja world war.


	3. Author's Note 1

Naruto No Rin'negan

A/N Hi, this isn't a chapter I just wanted you the readers, what you want to see in this story.

Please tell me what Main Summon you want for Naruto to use and What Kekkai Genkai should have (No Doujutsus) just specific releases.

I have put a poll on my page and the voting will end on the 29th December. Please vote!

The results will be shown in each chapter


	4. Author Note 2

Naruto No Rin'negan

By Mike-Parrott

Author Note: 2

I'm back!

Sorry it's been 3 months since I've published or even updated my story. Been busy with coursework deadlines/exams and break-ups, but yeah I'm back and i'm gonna start updating and publishing.

Thanks everybody for the reviews, favourite stories and favourite authors. I don't believe from just two chapters I have so many reviews and I'm people's favourite author.

But yeah even though this is just to inform you all about my return. I was wondering if anybody would want to be my beta reader and if anybody is good at writing lemons for my story in the upcoming future.

And thanks for everybody who voted in my poll (an extremely long time ago) and the top votes were Storm Release and the fox as summon. Even though I made that poll, after reading the majority of reviews I'm going to let him have every sub-element (lava, boil, wood etc.) But Ranton (Storm element) will be his main sub-element.

And because of it being his main I'm going to give Naruto the ability to use black lightning in the future. I'm a massive fan of Darui (manga character if you don't read it) and i will probably have Naruto be taught by Darui in the future after Nagato and Konan.

So thanks to all my viewers, reviewers and just people who love me!

New chapters are being wrote at the moment so their will be a weekly dosage of Naruto No Rin'negan for years!

Thanks guys keep reviewing


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